Added machinery to build Drudes and lone pairs.

Since lone pairs are integral parts of the residues
in the CHARMM Drude FF, I have added code to process
[virtual_sitesn] directives in the .rtp file to write
out these directives into the .top file.

The .tdb entries are still not done and this code remains
largely untested.

Change-Id: I54e76ad3b7e92cfc133a7d9187892ecf86a04256